TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv3671c/-:

update plot	correlation	link to info on gene
Rv2553c/-	(cc=0.7418)	info on Rv2553c/-
Rv1406/fmt	(cc=0.7245)	info on Rv1406/fmt
Rv3101c/ftsX	(cc=0.6982)	info on Rv3101c/ftsX
Rv1836c/-	(cc=0.6799)	info on Rv1836c/-
Rv3789/-	(cc=0.6647)	info on Rv3789/-
Rv3258c/-	(cc=0.6645)	info on Rv3258c/-
Rv0541c/-	(cc=0.6526)	info on Rv0541c/-
Rv1512/epiA	(cc=0.5941)	info on Rv1512/epiA
Rv2507/-	(cc=0.5853)	info on Rv2507/-
Rv1159/pimE	(cc=0.5699)	info on Rv1159/pimE

Correlation of Rv3671c/- with Rv2507/-

Normalized LFCs for Rv3671c/-:
(description and provenance of datasets)

	Rv3671c/-	Rv2507/-
Fe_supp_jason_reseq	0.415	0.218
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	-0.201	0.0
Rifampicin4	-0.374	0.0
Ethambutol3	-0.168	0.32
Meropenem3	-0.165	0.0
Vancomycin16	-0.366	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-4.019	-2.55
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.633	0.0
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.194	0.0
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	0.241	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.099	0.0
H37Rv_KO_MbtN	0.283	0.103
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-1.199	-1.565
delta_Rv3594	1.672	0.532
delta_Rv3717	0.429	0.159
delta_Rv3811	1.414	0.358
delta_Rv0954	0.627	-0.178
PonA1	-0.516	0.0
EccD1_KO	-1.417	0.73
EspI_KO	-0.724	1.184
PE35_KO	-0.137	1.467
PPE68_KO	-0.813	1.609
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.0
Rv0950ko	-2.044	-1.348
Rv1096ko	1.08	0.793
Rv3684ko	2.473	1.117
delta_otsA_trehalose	1.005	-0.079